Archive for October, 2010

In case you don’t know, Dienekes Pontikos has been posting a lot of analyses of availablepopulation geneticdata sets with the ADMIXTURE program. You can find his myriad posts under the ADMIXTURE-experiments tag. Below is a bar plot he generated today. To follow up a debate which occurred last spring, it does seem from several of his results that there is some evidence of Berber admixture among the Sephardic Jews.

When I was in college I would sometimes have late night conversations with the guys in my dorm, and the discussion would random-walk in very strange directions. During one of these quasi-salons a friend whose parents were from Korea expressed some surprise and disgust at the idea of wet earwax. It turns out he had not been aware of the fact that the majority of the people in the world have wet, sticky, earwax. I’d stumbled onto that datum in the course of my reading, and had to explain to most of the discussants that East Asians generally have dry earwax, while convincing my Korean American friend that wet earwax was not something that was totally abnormal. Earwax isn’t something we explore in polite conversation, so it makes sense that most people would be ignorant of the fact that there was inter-population variation on this phenotype.

But it doesn’t end there. Over the past five years the genetics of earwax has come back into the spotlight, because of its variation and what it can tell us about the history and evolution of humans since the Out of Africa event. Not only that, it seems the variation in earwax has some other phenotypiccorrelates. The SNPs in and around ABCC11 are a set where East Asians in particular show signs of being different from other world populations. The variants which are nearly fixed in East Asia around this locus are nearly disjoint in frequency with those in Africa. Here are the frequencies of the alleles of rs17822931 on ABCC11 from ALFRED:

In my post earlier in the week I mentioned the possible relationship between attitudes toward evolution and the causes and likelihood of Global Warming. I haven’t seen any survey data myself relating the two, so naturally I wanted to poke into the General Social Survey. Two variables of interest showed up, both from 2006:

I was floored today when the director of BGI told me they would soon reach a sequencing rate of 1000 (human) genomes per day (so, 10^5 to 10^6 genomes per year is right on the horizon). According to him, they can be profitable at a price of $5k per genome! [Clarification: I later learned this might mean at 10x coverage … not exactly sure, although I tried to get a more precise statement.]

[Q] 10) If in 10 years you could purchase your own full genome sequence for a month of your salary, would you do it? (assume privacy concerns are obviated)

[A] Yes.

It looks like I didn’t anticipate the rate of change in this area, as 10 years was also certainly too conservative or pessimistic. Dan MacArthur has given a plausible estimate of ~2 years for the realization of a $1,000 genome, but it looks like we’ll hit a genome at the cost of a month’s salary for a professional person on the order of months and not years.

The fresco to the left is the cover jacket illustration for Why we’re all Romans, a new cultural history which attempts to argue for the unique debts of Western civilization to Rome (in particular as a mediator of the wisdom of the Greeks and Hebrews). If you’re on the culturally conservative side it might be of some interest, it sports endorsements from a Fellow at the Hoover Institute and E. Christian Kopff. The fresco is from Pompeii, explaining its good state of preservation and present day fame and ubiquity. The man’s name is Terentius Neo, a wealthy merchant or magistrate apparently. The woman is presumed to be his wife. A strange question to throw out: am the only one who thinks that he resembles Laurence Fishburne? The fresco is used a lot because of its quality and prior fame, but I always start thinking of something ludicrous like The Matrix when I see it.

If you have some time to kill, the Paleo-Future weblog is really awesome. It shows what people thought the future was going to be like (often around the year 2000) from the 1870s through every decade of the 20th century. As usual with this sort of thing it tells you more about the salient aspects of a given time period, as people have a tendency of projecting contemporary fashions, technologies, and trends, rather than being able to anticipate innovation and changes of kind. Here’s a depiction of flying machines which dates to between 1900 and 1910:

The other day NPR’s Planet Money quipped that the gold bubble was going to burst soon, as they’d decided to buy gold. Well, perhaps Facebook is nearing its bursting point…I created a Gene Expression fan page. I don’t have a good sense of the great utility of this sort of thing…you can after all find the two GNXP weblogs on the world wide web pretty easily. And I feed the blog posts to twotwitter accounts. I can see the value-add of Facebook’s selective semi-permeability when it comes to the “social graph”, but less so for websites which have a robust presence on the internet. GNXP in some form has been around for over 8 years. I can’t but help feel that this is a flashier Geocities fan page.

There’s a lot of stuff you stumble upon via Google Public Data Explorer which you kind of knew, but is made all the more stark through quantitative display. For example, consider Saudi Arabia and Yemen. In gross national income per capita the difference between these two nations is one order of magnitude (PPP and nominal). Depending on the measure you use (PPP or nominal) the difference between the USA and Mexico is in the range of a factor of 3.5 to 5. Until recently most Americans did not know much about Yemen. It was famous for being the homeland of Osama bin Laden’s father and the Queen of Sheba.

About six months ago I read a history of modern Italy and was struck by a passage which observed that during the early years of the Italian state none of the prominent political leaders were practicing Roman Catholics. Part of this was specific to the history of the rise of modern Italy, Umberto I fought the Papacy, and so alienated the institution of the Church from the royal house and the state over which it ruled. But more generally many of the nationalists of the 19th century in Catholic Europe were of an anti-clerical bent. Only with the reconciliation of the Roman Catholic Church with the modern liberal democratic nation-state in the 20th century, and universal suffrage, have the political elites come to resemble the populace more in their religious sensibilities in these nations. And before you dismiss this as a European matter, observe that Andrew Jackson, our sixth president, was the first to have personal religious views in line with the American majority. As late as William Howard Taft in the early 20th century the United States had a head of state who rejected orthodox Christianity (he was a Unitarian Christian). Can we imagine that such a thing would come to pass without much controversy today? Mitt Romney has famously had to elide the yawning chasm between Mormonism and Nicene Christianity to be a viable candidate.

The point I’m trying to make here is that the paths of the arrows of history are more complex than we perceive them in our own moment in time. It is ironic that we in the United States are living through a period of secularization at the grassroots, while at the same time having to deal with the fact that all high level politicians have to pass through a de factoreligious litmus test of relatively stringent orthodoxy. The complexity of this sort of social phenomenon makes it exceedingly difficult to analyze and characterize in a pithy fashion. Too often when scholars and intellectuals speak of the history of religion they impose their own visions on the flux of human belief and behavior. Eric Kaufmann’s Shall the Religious Inherit the Earth is not such an argument. Rather, it is a cautious work which makes recourse to both robust theoretical models as well as a wide and rich set of empirical data. Kaufmann casts a very wide net in his attempt to retrieve a useful catch in terms of plausible and robust predictions. The central idea of the book is derived from the fact that the endogenous growth rates of religious segments of developed societies can often be rather high. The broader implication is that history moves in cycles, and that the current age of secularism is nearing its peak, and inevitable demographic forces will see the tide retreat.

How many people believe in evolution in this country? I’d like to see. I mean, I don’t know why it’s unreasonable to say this. I’m not God so I don’t know how God creates. I don’t think we came from monkeys. I think that’s ridiculous. I haven’t seen a half-monkey, half-person yet. Did evolution just stop? Did we all of sudden — there’s no other species that’s developing into half-human?

It’s like global warming. So I don’t know why it is so problematic for people to just so, I don’t know how God creates. I don’t know how we got here. If I get to the other side and God’s like, “You know what, you were a monkey once,” I’ll be shocked, but I’ll be like, “Whatever.”

First, Glenn Beck is an adult convert to the Mormon religion. Therefore if he is exalted to godhood he could create a universe of half-monkeys/half-men for kicks. Second, note the details of Beck’s background. He was raised Roman Catholic, and secular for most of his adulthood, before coming to the Mormon church. None of these affinities entails a rejection of evolution. You are probably well aware that the Roman Catholic church has made its peace, broadly speaking, with evolution. And there’s nothing about secularism which necessitates a rejection of evolution. But what about Mormonism? This is the peculiarity. Mormons are broadly sympathetic to Creationism, but there’s nothing in the religion’s teachings which imply this as being the orthodox position. This is why Mitt Romney can robustly support the teaching of evolution. So what’s going in?

My DonorsChoose page. Compared to previous years I’m kind of under-performing. I haven’t done any PBS-like incentives before, but perhaps I should. For example, anyone who gives $250 is owed a post from me on a topic of their choice of at least 2,000 words excluding quotations within the next 3 months. Those are just stray numbers thrown out there, but anyone interested? You’d have to rely on my good faith obviously, as I’m the final arbiter as to whether I’m gaming the metrics, but I’m an honest person about these sorts of things. It would probably be reasonable to do a graduated scale above a minimum threshold too.

One of the great geological landmarks on earth are the Himalayas. Not only are the Himalayas of importance in the domain of physical geography, but they are important in human geography as well. Just as South Asians and non-South Asians agree that the valley of the Indus and its tributaries bound the west of the Indian cultural world, so the Himalayas bound it on the north. Unlike many pre-modern constructions, such as the eastern boundary of Europe, the northern limit of South Asia is relatively clear and distinct. It is stark on a relief map; the flat Gangetic plain gives way to mountains. And it is stark a cultural map, the languages of northern India give way to those of the world of Tibet. The religion of northern India gives way to the Buddhism of Tibet. In terms of human geography I believe that one can argue that the Himalayan fringe around South Asia exhibits the greatest change of ancestrally informative gene frequencies over the smallest distance when you exclude those regions separated by water barriers. Unlike the Sahara the transect from the northern India to Chinese Tibet at any given point along the border is permanently inhabited, albeit sparsely at the heights.

And yet despite the geographical barriers people and ideas did move across the Himalaya. The cultural influences upon Tibet from India are obvious. The script of Tibet is derived from India, while its form of Buddhism is the direct descendant of the last efflorescence of that religion in northern India. But while culture moved north, I do not see much evidence genetically that South Asians have been significant as an influence. This is somewhat shocking when you realize these two facts: the population of the Tibetan Autonomous Region is on the order of 5-6 million, while that of northern South Asia around ~1 billion (including Pakistan and Bangladesh). A 200-fold difference. And yet there is evidence of admixture between the two groups exactly where you’d expect: in Nepal. Below is a figure from a recent paper which shows how South and East Asian populations relate to each other. I’ve highlighted the Nepali groups, which span the two larger classes:

Use Cash, Not Cards, To Buy Better Food? Another of the upsides of the “pain of paying.” I wonder if the effect will be transferred to debit cards as we move away from cash? Or, perhaps the effect is tied to the concreteness of a currency, and cash is just more concrete than debit cards. If you had gold ingots would there be more pain? And barter?

Food is a fraught topic. In How Pleasure Works Paul Bloom alludes to the thesis that while conservatives fixate on sexual purity, liberals fixate on culinary purity. For example, is it organic? What is the sourcing? Is it “authentic”? Obviously one can take issue with this characterization, especially its general class inflection (large swaths of the population buy what they can afford). Additionally, I doubt Hindus, Muslims and Jews who take a deep interest in the provenance, preparation, and substance of their food are liberals. What Bloom is noticing is actually a general human preoccupation which somehow has taken on a strange political valence in the United States. Somehow being conservative in this country has become aligned with a satisfaction with the mass-produced goods of the agricultural-industrial complex.* Some conservatives such as Rod Dreher have pushed back against this connotation, lengthily in his book Crunchy Cons.

Stepping away from politics, we are a diet obsessed culture broadly. Apparently Christina Hendricks is going on a diet, her aim being to lose 30 pounds. Diet fads come and go. The Atkins approach has faded of late, with the Paleolithic diet coming into fashion. A totally separate market segment, that of raw food, remains robustly popular. This was obvious when Richard Wrangham came out with Catching Fire: How Cooking Made Us Human; raw food enthusiasts would call in to talk shows where he was a guest, sometimes irritated that Wrangham was claiming that cooking was central to the emergence of modern humanity. His contention that raw food practitioners were healthy precisely because they don’t process as much of their nutritional intake because of the relatively coarse character of what they were consuming was clearly discomfiting to many of them. This is because it is at variance with some of the rationale for their diet. They are not cooking the food in part because they believe that that removes a great deal of nutritive value.

I was thinking about this while reading What is Global History? Offhand the author mentions bread-making as early as 20,000 years go in the process of asserting that many of the preconditions for an agricultural mode of production were already in existence before the end of the last Ice Age. I was surprised by this fact, having never encountered it before. Unfortunately there wasn’t a footnote which I could follow up on, so I thought no more of it. Imagine my curiosity when I stumble upon this paper in PNAS, Thirty thousand-year-old evidence of plant food processing:

A quintessentially sexy topic in biology is the origin of sex. Not only are biologists interested in it, but so is the public. Of Matt Ridley’s older books it is predictable that The Red Queen has the highest rank on Amazon. We humans have a fixation on sex, both in our public norms and our private actions. Why?

Because without a fixation on sex we would not be here. Celibates do not inherit the earth biologically. This answer emerges naturally from a Darwinian framework. And yet more deeply still: why sex for reproduction? Here I allude to the famous two-fold cost of sex. In dioecious species you have males and females, and males do not directly produce offspring. The increase of the population is constrained by the number of females in such lineages (male gametes are cheap). There is no such limitation in asexual lineages, where every individual can contribute to reproductive “primary production.” Additionally, the mating dance is another cost of sex. Individuals expend time and energy seeking out mates, and may have to compete and display for the attention of all. Why bother?

The answer on the broadest-scale seems to be variation. Variation in selective pressures, and variation in genes. Sex famously results in the shuffling of genetic permutations through recombination and segregation. In a world of protean change where one’s genes are critical to giving one the edge of fitness this constant flux of combinations results in more long term robusticity. What clones gain in proximate perfection, they lose when judged by the vicissitudes of the pressures of adaptation. In the present they flourish, but in the future they perish. Sex is the tortoise, clonal reproduction is the hare.

And yet science is more than just coarse generalities; biology especially so. The details of how sex emerges ad persists still remains to be fleshed out. The second volume of W. D. Hamilton’s collected papers, Narrow Roads of Gene Land, is the largest. Mostly because it was not edited appropriately (he died before it could be). But also perhaps because it is the volume most fixated upon the origin and persistence of sex, which is a broad and expansive topic.

The New York Times has a piece out on the “Hispanic Paradox”. The paradox is that American Hispanics are longer-lived than non-Hispanic whites, despite the relatively lower socioeconomic status of Hispanics (poorer, less educated). The paradox has been around for a while, and these stories tend to emerge whenever there’s a Census or CDC data release, as there is now. You can get the original data on the CDC website.

But I think one thing about the Hispanic Paradox that needs to be contextualized is that Hispanics are not special in manifesting this paradox. Throwing all non-Hispanic whites into one big pot aggregates real variation. The map on the left is from the paper Eight Americas: Investigating Mortality Disparities across Races, Counties, and Race-Counties in the United States. It shows the life expectancy by county for whites, Hispanic and non-Hispanic. You can see the Hispanic Paradox along the border; most Hispanics in Texas list their race as white, and so show up in these data. But you can also see what I’m talking about in terms of aggregation of non-Hispanic whites for Texas as well. See the counties in the center of Texas with elevated life expectancies? Take a look at this map on the distribution of German ancestry in the USA, and focus on Texas.

John Hawks is reporting that Leigh Van Valen passed away this weekend. I had the pleasure and honor of Leigh Van Valen being an occasional reader of my musings. He would leave comments as “leigh.” Here’s one which he left in February 2008:

Goldschmidt did a great deal more than hopeless monsters. I was with Dobzhansky when he heard of Goldschmidt’s death. I’ve preserved his comment: “A great geneticist has just died.”

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